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Genome sequencing of SARS-COV-2 can help with contact tracing for COVID-19: studies reported in WaPo

2020-10-13
SARS-COV-2 particles emerging from a dying cell: EM by NIAID

These reports in The Washington Post describe how genome sequencing can help speed contact tracing for COVID-19, an effort that is otherwise fraught with difficulty. Contact tracing is limited by tracers’ ability to get information from people who may not be willing to talk or who do not remember with whom they came into contact. Having an accurate sequence can narrow down the number of people who were potential contacts or were infected by the same person.

Other countries have done much better than the US, not only in contact tracing by interviews, but also in sequencing the genomes of many more individual virus isolates.

The new article in WaPo (available free at the link) describes a fictional example of how sequencing helps with contact tracing, using novel graphics to help explain the process:

Imagine a place where politicians and public health experts use every tool at their disposal to contain the coronavirus.

Welcome to the fictional town of Scienceville.

https://www.washingtonpost.com/graphics/2020/health/coronavirus-genetic-code/

I strongly recommend this article to anyone interested in how we can use science to get out of this pandemic more quickly.

A concrete example of how the method works was described in this preprint published on MedRxiv on August 25, 2020. The preprint was also discussed in this story on WaPo. An outbreak in Boston that eventually spread to thousands of people was analyzed by looking at 772 viral genomes, all from within the first week of its spread. Over 80 separate introductions of the virus into Massachusetts were revealed.

Not only do viruses mutate as they are transmitted from person to person, but several variants of a virus may co-infect a single person. This preprint published on BioRxiv (updated on June 2, 2020) discusses significant variation of the virus within individual patients.

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